CRAN Package Check Results for Package mpwR

Last updated on 2022-12-19 07:53:34 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.0 11.61 192.76 204.37 ERROR
r-devel-linux-x86_64-debian-gcc 0.1.0 7.97 140.42 148.39 ERROR
r-devel-linux-x86_64-fedora-clang 0.1.0 262.04 ERROR
r-devel-linux-x86_64-fedora-gcc 0.1.0 245.39 ERROR
r-devel-windows-x86_64 0.1.0 28.00 233.00 261.00 ERROR
r-patched-linux-x86_64 0.1.0 8.26 185.77 194.03 ERROR
r-release-linux-x86_64 0.1.0 11.65 180.50 192.15 ERROR
r-release-macos-arm64 0.1.0 60.00 OK
r-release-macos-x86_64 0.1.0 79.00 OK
r-release-windows-x86_64 0.1.0 16.00 233.00 249.00 ERROR
r-oldrel-macos-arm64 0.1.0 50.00 OK
r-oldrel-macos-x86_64 0.1.0 81.00 OK
r-oldrel-windows-ix86+x86_64 0.1.0 29.00 224.00 253.00 ERROR

Check Details

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in 'mpwR-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: get_Upset_list
    > ### Title: Generate Upset list
    > ### Aliases: get_Upset_list
    >
    > ### ** Examples
    >
    > # Load libraries
    > library(tibble)
    > library(magrittr)
    > library(stringr)
    >
    > # Example data
    > data <- list(
    + DIANN = list(
    + filename = "B",
    + software = "DIA-NN",
    + data = list(
    + "DIA-NN" = tibble::tibble(
    + Run_mpwR = rep(c("A","B"), times = 10),
    + Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
    + Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
    + Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
    + ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
    + )
    + )
    + ),
    + Spectronaut = list(
    + filename = "C",
    + software = "Spectronaut",
    + data = list(
    + "Spectronaut" = tibble::tibble(
    + Run_mpwR = rep(c("A","B"), times = 15),
    + Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
    + Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
    + ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
    + )
    + )
    + )
    + )
    >
    > # Result
    > output <- get_Upset_list(
    + input_list = data,
    + level = "Precursor.IDs"
    + )
    Error in `stringr::str_detect()`:
    ! `pattern` can't be the empty string (`""`).
    Backtrace:
     x
     1. \-mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs")
     2. +-base::which(...)
     3. \-stringr::str_detect(string = names(output_list), pattern = "")
     4. \-stringr:::no_empty()
     5. \-cli::cli_abort(...)
     6. \-rlang::abort(...)
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.0
Check: tests
Result: ERROR
     Running 'testthat.R' [88s/117s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(mpwR)
     >
     > test_check("mpwR")
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on peptide-level.
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on proteingroup-level.
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For MaxQuant evidence.txt - the following column need to be present: Raw file
     For MaxQuant evidence.txt - the following column need to be present: Proteins
     For MaxQuant evidence.txt - the following column need to be present: Modified sequence
     For MaxQuant evidence.txt - the following column need to be present: Sequence
     For MaxQuant evidence.txt - the following column need to be present: Missed cleavages
     For MaxQuant evidence.txt - the following column need to be present: Charge
     For MaxQuant evidence.txt - the following column need to be present: Retention time
     For MaxQuant evidence.txt - the following column need to be present: Potential contaminant
     For MaxQuant evidence.txt - the following column need to be present: Reverse
    
     For MaxQuant proteinGroups.txt input - the following column need to be present: Protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Majority protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Peptide counts (all)
     For MaxQuant proteinGroups.txt input - the following column need to be present: Potential contaminant
     For MaxQuant proteinGroups.txt input - the following column need to be present: Reverse
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For PD PSMs.txt - the following column need to be present: Confidence
     For PD PSMs.txt - the following column need to be present: Spectrum File
     For PD PSMs.txt - the following column need to be present: Protein Accessions
     For PD PSMs.txt - the following column need to be present: Annotated Sequence
     For PD PSMs.txt - the following column need to be present: Modifications
     For PD PSMs.txt - the following column need to be present: Number of Missed Cleavages
     For PD PSMs.txt - the following column need to be present: Charge
     For PD PSMs.txt - the following column need to be present: RT in min
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For plotting density: CV_Retention.time_mpwR is not detected in submitted data.
     For plotting density: CV_Peptide_LFQ_mpwR is not detected in submitted data.
     For plotting density: CV_ProteinGroup_LFQ_mpwR is not detected in submitted data.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting stacked barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting boxplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
    
     == Failed tests ================================================================
     -- Error ('test_Upset.R:72'): get_Upset_list works -----------------------------
     Error in `stringr::str_detect(string = names(output_list), pattern = "")`: `pattern` can't be the empty string (`""`).
     Backtrace:
     x
     1. \-mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs") at test_Upset.R:72:3
     2. +-base::which(...)
     3. \-stringr::str_detect(string = names(output_list), pattern = "")
     4. \-stringr:::no_empty()
     5. \-cli::cli_abort(...)
     6. \-rlang::abort(...)
    
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
    Error(s) in re-building vignettes:
     ...
    --- re-building 'Import.Rmd' using rmarkdown
    --- finished re-building 'Import.Rmd'
    
    --- re-building 'Requirements.Rmd' using rmarkdown
    --- finished re-building 'Requirements.Rmd'
    
    --- re-building 'Workflow.Rmd' using rmarkdown
    Quitting from lines 225-226 (Workflow.Rmd)
    Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
    `pattern` can't be the empty string (`""`).
    --- failed re-building 'Workflow.Rmd'
    
    SUMMARY: processing the following file failed:
     'Workflow.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in ‘mpwR-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: get_Upset_list
    > ### Title: Generate Upset list
    > ### Aliases: get_Upset_list
    >
    > ### ** Examples
    >
    > # Load libraries
    > library(tibble)
    > library(magrittr)
    > library(stringr)
    >
    > # Example data
    > data <- list(
    + DIANN = list(
    + filename = "B",
    + software = "DIA-NN",
    + data = list(
    + "DIA-NN" = tibble::tibble(
    + Run_mpwR = rep(c("A","B"), times = 10),
    + Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
    + Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
    + Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
    + ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
    + )
    + )
    + ),
    + Spectronaut = list(
    + filename = "C",
    + software = "Spectronaut",
    + data = list(
    + "Spectronaut" = tibble::tibble(
    + Run_mpwR = rep(c("A","B"), times = 15),
    + Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
    + Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
    + ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
    + )
    + )
    + )
    + )
    >
    > # Result
    > output <- get_Upset_list(
    + input_list = data,
    + level = "Precursor.IDs"
    + )
    Error in `stringr::str_detect()`:
    ! `pattern` can't be the empty string (`""`).
    Backtrace:
     ▆
     1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs")
     2. ├─base::which(...)
     3. └─stringr::str_detect(string = names(output_list), pattern = "")
     4. └─stringr:::no_empty()
     5. └─cli::cli_abort(...)
     6. └─rlang::abort(...)
    Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [63s/105s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(mpwR)
     >
     > test_check("mpwR")
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on peptide-level.
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on proteingroup-level.
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For MaxQuant evidence.txt - the following column need to be present: Raw file
     For MaxQuant evidence.txt - the following column need to be present: Proteins
     For MaxQuant evidence.txt - the following column need to be present: Modified sequence
     For MaxQuant evidence.txt - the following column need to be present: Sequence
     For MaxQuant evidence.txt - the following column need to be present: Missed cleavages
     For MaxQuant evidence.txt - the following column need to be present: Charge
     For MaxQuant evidence.txt - the following column need to be present: Retention time
     For MaxQuant evidence.txt - the following column need to be present: Potential contaminant
     For MaxQuant evidence.txt - the following column need to be present: Reverse
    
     For MaxQuant proteinGroups.txt input - the following column need to be present: Protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Majority protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Peptide counts (all)
     For MaxQuant proteinGroups.txt input - the following column need to be present: Potential contaminant
     For MaxQuant proteinGroups.txt input - the following column need to be present: Reverse
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For PD PSMs.txt - the following column need to be present: Confidence
     For PD PSMs.txt - the following column need to be present: Spectrum File
     For PD PSMs.txt - the following column need to be present: Protein Accessions
     For PD PSMs.txt - the following column need to be present: Annotated Sequence
     For PD PSMs.txt - the following column need to be present: Modifications
     For PD PSMs.txt - the following column need to be present: Number of Missed Cleavages
     For PD PSMs.txt - the following column need to be present: Charge
     For PD PSMs.txt - the following column need to be present: RT in min
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For plotting density: CV_Retention.time_mpwR is not detected in submitted data.
     For plotting density: CV_Peptide_LFQ_mpwR is not detected in submitted data.
     For plotting density: CV_ProteinGroup_LFQ_mpwR is not detected in submitted data.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting stacked barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting boxplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error ('test_Upset.R:72'): get_Upset_list works ─────────────────────────────
     Error in `stringr::str_detect(string = names(output_list), pattern = "")`: `pattern` can't be the empty string (`""`).
     Backtrace:
     ▆
     1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs") at test_Upset.R:72:3
     2. ├─base::which(...)
     3. └─stringr::str_detect(string = names(output_list), pattern = "")
     4. └─stringr:::no_empty()
     5. └─cli::cli_abort(...)
     6. └─rlang::abort(...)
    
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in ‘mpwR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: get_Upset_list
    > ### Title: Generate Upset list
    > ### Aliases: get_Upset_list
    >
    > ### ** Examples
    >
    > # Load libraries
    > library(tibble)
    > library(magrittr)
    > library(stringr)
    >
    > # Example data
    > data <- list(
    + DIANN = list(
    + filename = "B",
    + software = "DIA-NN",
    + data = list(
    + "DIA-NN" = tibble::tibble(
    + Run_mpwR = rep(c("A","B"), times = 10),
    + Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
    + Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
    + Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
    + ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
    + )
    + )
    + ),
    + Spectronaut = list(
    + filename = "C",
    + software = "Spectronaut",
    + data = list(
    + "Spectronaut" = tibble::tibble(
    + Run_mpwR = rep(c("A","B"), times = 15),
    + Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
    + Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
    + ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
    + )
    + )
    + )
    + )
    >
    > # Result
    > output <- get_Upset_list(
    + input_list = data,
    + level = "Precursor.IDs"
    + )
    Error in `stringr::str_detect()`:
    ! `pattern` can't be the empty string (`""`).
    Backtrace:
     ▆
     1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs")
     2. ├─base::which(...)
     3. └─stringr::str_detect(string = names(output_list), pattern = "")
     4. └─stringr:::no_empty()
     5. └─cli::cli_abort(...)
     6. └─rlang::abort(...)
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [109s/277s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(mpwR)
     >
     > test_check("mpwR")
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on peptide-level.
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on proteingroup-level.
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For MaxQuant evidence.txt - the following column need to be present: Raw file
     For MaxQuant evidence.txt - the following column need to be present: Proteins
     For MaxQuant evidence.txt - the following column need to be present: Modified sequence
     For MaxQuant evidence.txt - the following column need to be present: Sequence
     For MaxQuant evidence.txt - the following column need to be present: Missed cleavages
     For MaxQuant evidence.txt - the following column need to be present: Charge
     For MaxQuant evidence.txt - the following column need to be present: Retention time
     For MaxQuant evidence.txt - the following column need to be present: Potential contaminant
     For MaxQuant evidence.txt - the following column need to be present: Reverse
    
     For MaxQuant proteinGroups.txt input - the following column need to be present: Protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Majority protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Peptide counts (all)
     For MaxQuant proteinGroups.txt input - the following column need to be present: Potential contaminant
     For MaxQuant proteinGroups.txt input - the following column need to be present: Reverse
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For PD PSMs.txt - the following column need to be present: Confidence
     For PD PSMs.txt - the following column need to be present: Spectrum File
     For PD PSMs.txt - the following column need to be present: Protein Accessions
     For PD PSMs.txt - the following column need to be present: Annotated Sequence
     For PD PSMs.txt - the following column need to be present: Modifications
     For PD PSMs.txt - the following column need to be present: Number of Missed Cleavages
     For PD PSMs.txt - the following column need to be present: Charge
     For PD PSMs.txt - the following column need to be present: RT in min
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For plotting density: CV_Retention.time_mpwR is not detected in submitted data.
     For plotting density: CV_Peptide_LFQ_mpwR is not detected in submitted data.
     For plotting density: CV_ProteinGroup_LFQ_mpwR is not detected in submitted data.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting stacked barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting boxplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error ('test_Upset.R:72'): get_Upset_list works ─────────────────────────────
     Error in `stringr::str_detect(string = names(output_list), pattern = "")`: `pattern` can't be the empty string (`""`).
     Backtrace:
     ▆
     1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs") at test_Upset.R:72:3
     2. ├─base::which(...)
     3. └─stringr::str_detect(string = names(output_list), pattern = "")
     4. └─stringr:::no_empty()
     5. └─cli::cli_abort(...)
     6. └─rlang::abort(...)
    
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
    Error(s) in re-building vignettes:
    --- re-building ‘Import.Rmd’ using rmarkdown
    --- finished re-building ‘Import.Rmd’
    
    --- re-building ‘Requirements.Rmd’ using rmarkdown
    --- finished re-building ‘Requirements.Rmd’
    
    --- re-building ‘Workflow.Rmd’ using rmarkdown
    Quitting from lines 225-226 (Workflow.Rmd)
    Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
    `pattern` can't be the empty string (`""`).
    --- failed re-building ‘Workflow.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘Workflow.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [99s/113s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(mpwR)
     >
     > test_check("mpwR")
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on peptide-level.
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on proteingroup-level.
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For MaxQuant evidence.txt - the following column need to be present: Raw file
     For MaxQuant evidence.txt - the following column need to be present: Proteins
     For MaxQuant evidence.txt - the following column need to be present: Modified sequence
     For MaxQuant evidence.txt - the following column need to be present: Sequence
     For MaxQuant evidence.txt - the following column need to be present: Missed cleavages
     For MaxQuant evidence.txt - the following column need to be present: Charge
     For MaxQuant evidence.txt - the following column need to be present: Retention time
     For MaxQuant evidence.txt - the following column need to be present: Potential contaminant
     For MaxQuant evidence.txt - the following column need to be present: Reverse
    
     For MaxQuant proteinGroups.txt input - the following column need to be present: Protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Majority protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Peptide counts (all)
     For MaxQuant proteinGroups.txt input - the following column need to be present: Potential contaminant
     For MaxQuant proteinGroups.txt input - the following column need to be present: Reverse
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For PD PSMs.txt - the following column need to be present: Confidence
     For PD PSMs.txt - the following column need to be present: Spectrum File
     For PD PSMs.txt - the following column need to be present: Protein Accessions
     For PD PSMs.txt - the following column need to be present: Annotated Sequence
     For PD PSMs.txt - the following column need to be present: Modifications
     For PD PSMs.txt - the following column need to be present: Number of Missed Cleavages
     For PD PSMs.txt - the following column need to be present: Charge
     For PD PSMs.txt - the following column need to be present: RT in min
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For plotting density: CV_Retention.time_mpwR is not detected in submitted data.
     For plotting density: CV_Peptide_LFQ_mpwR is not detected in submitted data.
     For plotting density: CV_ProteinGroup_LFQ_mpwR is not detected in submitted data.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting stacked barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting boxplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error ('test_Upset.R:72'): get_Upset_list works ─────────────────────────────
     Error in `stringr::str_detect(string = names(output_list), pattern = "")`: `pattern` can't be the empty string (`""`).
     Backtrace:
     ▆
     1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs") at test_Upset.R:72:3
     2. ├─base::which(...)
     3. └─stringr::str_detect(string = names(output_list), pattern = "")
     4. └─stringr:::no_empty()
     5. └─cli::cli_abort(...)
     6. └─rlang::abort(...)
    
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.1.0
Check: tests
Result: ERROR
     Running 'testthat.R' [86s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(mpwR)
     >
     > test_check("mpwR")
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on peptide-level.
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on proteingroup-level.
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For MaxQuant evidence.txt - the following column need to be present: Raw file
     For MaxQuant evidence.txt - the following column need to be present: Proteins
     For MaxQuant evidence.txt - the following column need to be present: Modified sequence
     For MaxQuant evidence.txt - the following column need to be present: Sequence
     For MaxQuant evidence.txt - the following column need to be present: Missed cleavages
     For MaxQuant evidence.txt - the following column need to be present: Charge
     For MaxQuant evidence.txt - the following column need to be present: Retention time
     For MaxQuant evidence.txt - the following column need to be present: Potential contaminant
     For MaxQuant evidence.txt - the following column need to be present: Reverse
    
     For MaxQuant proteinGroups.txt input - the following column need to be present: Protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Majority protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Peptide counts (all)
     For MaxQuant proteinGroups.txt input - the following column need to be present: Potential contaminant
     For MaxQuant proteinGroups.txt input - the following column need to be present: Reverse
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For PD PSMs.txt - the following column need to be present: Confidence
     For PD PSMs.txt - the following column need to be present: Spectrum File
     For PD PSMs.txt - the following column need to be present: Protein Accessions
     For PD PSMs.txt - the following column need to be present: Annotated Sequence
     For PD PSMs.txt - the following column need to be present: Modifications
     For PD PSMs.txt - the following column need to be present: Number of Missed Cleavages
     For PD PSMs.txt - the following column need to be present: Charge
     For PD PSMs.txt - the following column need to be present: RT in min
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For plotting density: CV_Retention.time_mpwR is not detected in submitted data.
     For plotting density: CV_Peptide_LFQ_mpwR is not detected in submitted data.
     For plotting density: CV_ProteinGroup_LFQ_mpwR is not detected in submitted data.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting stacked barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting boxplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error ('test_Upset.R:72'): get_Upset_list works ─────────────────────────────
     Error in `stringr::str_detect(string = names(output_list), pattern = "")`: `pattern` can't be the empty string (`""`).
     Backtrace:
     ▆
     1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs") at test_Upset.R:72:3
     2. ├─base::which(...)
     3. └─stringr::str_detect(string = names(output_list), pattern = "")
     4. └─stringr:::no_empty()
     5. └─cli::cli_abort(...)
     6. └─rlang::abort(...)
    
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-windows-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [84s/99s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(mpwR)
     >
     > test_check("mpwR")
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on peptide-level.
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on proteingroup-level.
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For MaxQuant evidence.txt - the following column need to be present: Raw file
     For MaxQuant evidence.txt - the following column need to be present: Proteins
     For MaxQuant evidence.txt - the following column need to be present: Modified sequence
     For MaxQuant evidence.txt - the following column need to be present: Sequence
     For MaxQuant evidence.txt - the following column need to be present: Missed cleavages
     For MaxQuant evidence.txt - the following column need to be present: Charge
     For MaxQuant evidence.txt - the following column need to be present: Retention time
     For MaxQuant evidence.txt - the following column need to be present: Potential contaminant
     For MaxQuant evidence.txt - the following column need to be present: Reverse
    
     For MaxQuant proteinGroups.txt input - the following column need to be present: Protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Majority protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Peptide counts (all)
     For MaxQuant proteinGroups.txt input - the following column need to be present: Potential contaminant
     For MaxQuant proteinGroups.txt input - the following column need to be present: Reverse
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For PD PSMs.txt - the following column need to be present: Confidence
     For PD PSMs.txt - the following column need to be present: Spectrum File
     For PD PSMs.txt - the following column need to be present: Protein Accessions
     For PD PSMs.txt - the following column need to be present: Annotated Sequence
     For PD PSMs.txt - the following column need to be present: Modifications
     For PD PSMs.txt - the following column need to be present: Number of Missed Cleavages
     For PD PSMs.txt - the following column need to be present: Charge
     For PD PSMs.txt - the following column need to be present: RT in min
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For plotting density: CV_Retention.time_mpwR is not detected in submitted data.
     For plotting density: CV_Peptide_LFQ_mpwR is not detected in submitted data.
     For plotting density: CV_ProteinGroup_LFQ_mpwR is not detected in submitted data.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting stacked barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting boxplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error ('test_Upset.R:72'): get_Upset_list works ─────────────────────────────
     Error in `stringr::str_detect(string = names(output_list), pattern = "")`: `pattern` can't be the empty string (`""`).
     Backtrace:
     ▆
     1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs") at test_Upset.R:72:3
     2. ├─base::which(...)
     3. └─stringr::str_detect(string = names(output_list), pattern = "")
     4. └─stringr:::no_empty()
     5. └─cli::cli_abort(...)
     6. └─rlang::abort(...)
    
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
     Error: Test failures
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [83s/93s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(mpwR)
     >
     > test_check("mpwR")
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on peptide-level.
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on proteingroup-level.
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For MaxQuant evidence.txt - the following column need to be present: Raw file
     For MaxQuant evidence.txt - the following column need to be present: Proteins
     For MaxQuant evidence.txt - the following column need to be present: Modified sequence
     For MaxQuant evidence.txt - the following column need to be present: Sequence
     For MaxQuant evidence.txt - the following column need to be present: Missed cleavages
     For MaxQuant evidence.txt - the following column need to be present: Charge
     For MaxQuant evidence.txt - the following column need to be present: Retention time
     For MaxQuant evidence.txt - the following column need to be present: Potential contaminant
     For MaxQuant evidence.txt - the following column need to be present: Reverse
    
     For MaxQuant proteinGroups.txt input - the following column need to be present: Protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Majority protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Peptide counts (all)
     For MaxQuant proteinGroups.txt input - the following column need to be present: Potential contaminant
     For MaxQuant proteinGroups.txt input - the following column need to be present: Reverse
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For PD PSMs.txt - the following column need to be present: Confidence
     For PD PSMs.txt - the following column need to be present: Spectrum File
     For PD PSMs.txt - the following column need to be present: Protein Accessions
     For PD PSMs.txt - the following column need to be present: Annotated Sequence
     For PD PSMs.txt - the following column need to be present: Modifications
     For PD PSMs.txt - the following column need to be present: Number of Missed Cleavages
     For PD PSMs.txt - the following column need to be present: Charge
     For PD PSMs.txt - the following column need to be present: RT in min
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For plotting density: CV_Retention.time_mpwR is not detected in submitted data.
     For plotting density: CV_Peptide_LFQ_mpwR is not detected in submitted data.
     For plotting density: CV_ProteinGroup_LFQ_mpwR is not detected in submitted data.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting stacked barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting boxplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error ('test_Upset.R:72'): get_Upset_list works ─────────────────────────────
     Error in `stringr::str_detect(string = names(output_list), pattern = "")`: `pattern` can't be the empty string (`""`).
     Backtrace:
     ▆
     1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs") at test_Upset.R:72:3
     2. ├─base::which(...)
     3. └─stringr::str_detect(string = names(output_list), pattern = "")
     4. └─stringr:::no_empty()
     5. └─cli::cli_abort(...)
     6. └─rlang::abort(...)
    
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
     Error: Test failures
     Execution halted
Flavor: r-release-linux-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running 'testthat.R' [90s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(mpwR)
     >
     > test_check("mpwR")
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on peptide-level.
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on proteingroup-level.
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For MaxQuant evidence.txt - the following column need to be present: Raw file
     For MaxQuant evidence.txt - the following column need to be present: Proteins
     For MaxQuant evidence.txt - the following column need to be present: Modified sequence
     For MaxQuant evidence.txt - the following column need to be present: Sequence
     For MaxQuant evidence.txt - the following column need to be present: Missed cleavages
     For MaxQuant evidence.txt - the following column need to be present: Charge
     For MaxQuant evidence.txt - the following column need to be present: Retention time
     For MaxQuant evidence.txt - the following column need to be present: Potential contaminant
     For MaxQuant evidence.txt - the following column need to be present: Reverse
    
     For MaxQuant proteinGroups.txt input - the following column need to be present: Protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Majority protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Peptide counts (all)
     For MaxQuant proteinGroups.txt input - the following column need to be present: Potential contaminant
     For MaxQuant proteinGroups.txt input - the following column need to be present: Reverse
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For PD PSMs.txt - the following column need to be present: Confidence
     For PD PSMs.txt - the following column need to be present: Spectrum File
     For PD PSMs.txt - the following column need to be present: Protein Accessions
     For PD PSMs.txt - the following column need to be present: Annotated Sequence
     For PD PSMs.txt - the following column need to be present: Modifications
     For PD PSMs.txt - the following column need to be present: Number of Missed Cleavages
     For PD PSMs.txt - the following column need to be present: Charge
     For PD PSMs.txt - the following column need to be present: RT in min
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For plotting density: CV_Retention.time_mpwR is not detected in submitted data.
     For plotting density: CV_Peptide_LFQ_mpwR is not detected in submitted data.
     For plotting density: CV_ProteinGroup_LFQ_mpwR is not detected in submitted data.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting stacked barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting boxplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error ('test_Upset.R:72'): get_Upset_list works ─────────────────────────────
     Error in `stringr::str_detect(string = names(output_list), pattern = "")`: `pattern` can't be the empty string (`""`).
     Backtrace:
     ▆
     1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs") at test_Upset.R:72:3
     2. ├─base::which(...)
     3. └─stringr::str_detect(string = names(output_list), pattern = "")
     4. └─stringr:::no_empty()
     5. └─cli::cli_abort(...)
     6. └─rlang::abort(...)
    
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
     Error: Test failures
     Execution halted
Flavor: r-release-windows-x86_64

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in 'mpwR-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: get_Upset_list
    > ### Title: Generate Upset list
    > ### Aliases: get_Upset_list
    >
    > ### ** Examples
    >
    > # Load libraries
    > library(tibble)
    > library(magrittr)
    > library(stringr)
    >
    > # Example data
    > data <- list(
    + DIANN = list(
    + filename = "B",
    + software = "DIA-NN",
    + data = list(
    + "DIA-NN" = tibble::tibble(
    + Run_mpwR = rep(c("A","B"), times = 10),
    + Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
    + Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
    + Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
    + ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
    + )
    + )
    + ),
    + Spectronaut = list(
    + filename = "C",
    + software = "Spectronaut",
    + data = list(
    + "Spectronaut" = tibble::tibble(
    + Run_mpwR = rep(c("A","B"), times = 15),
    + Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
    + Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
    + ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
    + )
    + )
    + )
    + )
    >
    > # Result
    > output <- get_Upset_list(
    + input_list = data,
    + level = "Precursor.IDs"
    + )
    Error in `stringr::str_detect()`:
    ! `pattern` can't be the empty string (`""`).
    Backtrace:
     x
     1. \-mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs")
     2. +-base::which(...)
     3. \-stringr::str_detect(string = names(output_list), pattern = "")
     4. \-stringr:::no_empty()
     5. \-cli::cli_abort(...)
     6. \-rlang::abort(...)
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running 'testthat.R' [96s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(mpwR)
     >
     > test_check("mpwR")
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on peptide-level.
     For DIA-NN no quantitative LFQ data on peptide-level.
     For PD no quantitative LFQ data on proteingroup-level.
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For ProteinGroup.IDs - No flowTraceR filtering applied
     For MaxQuant evidence.txt - the following column need to be present: Raw file
     For MaxQuant evidence.txt - the following column need to be present: Proteins
     For MaxQuant evidence.txt - the following column need to be present: Modified sequence
     For MaxQuant evidence.txt - the following column need to be present: Sequence
     For MaxQuant evidence.txt - the following column need to be present: Missed cleavages
     For MaxQuant evidence.txt - the following column need to be present: Charge
     For MaxQuant evidence.txt - the following column need to be present: Retention time
     For MaxQuant evidence.txt - the following column need to be present: Potential contaminant
     For MaxQuant evidence.txt - the following column need to be present: Reverse
    
     For MaxQuant proteinGroups.txt input - the following column need to be present: Protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Majority protein IDs
     For MaxQuant proteinGroups.txt input - the following column need to be present: Peptide counts (all)
     For MaxQuant proteinGroups.txt input - the following column need to be present: Potential contaminant
     For MaxQuant proteinGroups.txt input - the following column need to be present: Reverse
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For DIA-NN input - the following column need to be present: Run
     For DIA-NN input - the following column need to be present: Protein.Group
     For DIA-NN input - the following column need to be present: Protein.Ids
     For DIA-NN input - the following column need to be present: Modified.Sequence
     For DIA-NN input - the following column need to be present: Stripped.Sequence
     For DIA-NN input - the following column need to be present: Precursor.Id
     For DIA-NN input - the following column need to be present: Precursor.Charge
     For DIA-NN input - the following column need to be present: RT
     For DIA-NN input - the following column need to be present: PG.MaxLFQ
    
     For PD PSMs.txt - the following column need to be present: Confidence
     For PD PSMs.txt - the following column need to be present: Spectrum File
     For PD PSMs.txt - the following column need to be present: Protein Accessions
     For PD PSMs.txt - the following column need to be present: Annotated Sequence
     For PD PSMs.txt - the following column need to be present: Modifications
     For PD PSMs.txt - the following column need to be present: Number of Missed Cleavages
     For PD PSMs.txt - the following column need to be present: Charge
     For PD PSMs.txt - the following column need to be present: RT in min
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
     For PD PeptideGroups.txt - the following column need to be present: Peptide Groups Peptide Group ID
     For PD PeptideGroups.txt - the following column need to be present: Confidence
     For PD PeptideGroups.txt - the following column need to be present: Sequence
     For PD PeptideGroups.txt - the following column need to be present: Modifications
     For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD Proteins.txt - the following column(s) need to be present: Found in Sample
     For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID
     For PD Proteins.txt - the following column need to be present: Accession
     For PD Proteins.txt - the following column need to be present: Description
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
     For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID
     For PD ProteinGroups.txt - the following column need to be present: Group Description
     For PD ProteinGroups.txt - the following column need to be present: Number of Proteins
     For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides
    
     For plotting density: CV_Retention.time_mpwR is not detected in submitted data.
     For plotting density: CV_Peptide_LFQ_mpwR is not detected in submitted data.
     For plotting density: CV_ProteinGroup_LFQ_mpwR is not detected in submitted data.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting stacked barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     For plotting boxplot: Only NA detected for Protein.IDs! Not included in vizualisation.
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
    
     == Failed tests ================================================================
     -- Error ('test_Upset.R:72'): get_Upset_list works -----------------------------
     Error in `stringr::str_detect(string = names(output_list), pattern = "")`: `pattern` can't be the empty string (`""`).
     Backtrace:
     x
     1. \-mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs") at test_Upset.R:72:3
     2. +-base::which(...)
     3. \-stringr::str_detect(string = names(output_list), pattern = "")
     4. \-stringr:::no_empty()
     5. \-cli::cli_abort(...)
     6. \-rlang::abort(...)
    
     [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.1.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'Import.Rmd' using rmarkdown
    --- finished re-building 'Import.Rmd'
    
    --- re-building 'Requirements.Rmd' using rmarkdown
    --- finished re-building 'Requirements.Rmd'
    
    --- re-building 'Workflow.Rmd' using rmarkdown
    Quitting from lines 225-226 (Workflow.Rmd)
    Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
    `pattern` can't be the empty string (`""`).
    --- failed re-building 'Workflow.Rmd'
    
    SUMMARY: processing the following file failed:
     'Workflow.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64